Alarm puts deity in charge (5)
I believe the answer is:
panic
'alarm' is the definition.
(alarm can mean panic or worry)
'deity in charge' is the wordplay.
'deity' becomes 'pan' (Pan is an example).
'in charge' becomes 'ic' (abbreviation for 'in charge').
'pan'+'ic'='PANIC'
'puts' acts as a link.
(Other definitions for panic that I've seen before include "general alarm" , "Sudden extreme anxiety" , "Agitation" , "Sudden overpowering fright" , "Losing one's head" .)